In other words, if the bad guys with guns coerce Apple to mint them a cert, they could simply replace your known good binary with a crocked one signed with the new key, and your phone will happily run it. Getting that binary onto your phone is an exercise left to the reader, but there are many means, legal and otherwise, that could be employed to make that happen.
If your privacy means your life is on the line, you probably shouldn't be running stock Android or iOS. (And depending on how you feel about basebands, any modern smartphone, period.)